Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate GFF2063 HP15_2019 iron-containing alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Marino:GFF2063 Length = 385 Score = 274 bits (700), Expect = 4e-78 Identities = 162/376 (43%), Positives = 235/376 (62%), Gaps = 14/376 (3%) Query: 17 GALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPLET 76 G +L VK K +L++TDP LVK GL+D T+ L + G ++ VV +PP+ Sbjct: 17 GVTHRLGQIVKEHMGKKVLLVTDPGLVKAGLLDVATNSLNEAGVKYELFDGVVADPPVSV 76 Query: 77 GEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGLPK 136 E A+A AR+ D VIG GGGS++D+AKL A+L + + D + G + K LP Sbjct: 77 VEAALADAREAGVDGVIGFGGGSSMDVAKLIALLIGGEEKLDD---VYGVGQAKGKRLPL 133 Query: 137 ILIPTTSGTGSEVTNISVLSL-ETTKDVVTHDYLLADVAIVDPQLTVSVPPRVTAATGID 195 I IPTT+GTGSEVT IS++++ ET K V LL D+A++D +LT+ +P VTAATGID Sbjct: 134 IQIPTTAGTGSEVTPISIITVGETEKKGVVAPQLLPDIALLDAELTLGLPAHVTAATGID 193 Query: 196 ALTHAVEAYVSVNAS--PTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAGL 253 A+ HA+E+Y S +A+ P S LA A+RL+ ++ AV +GS+ +AR DM G+ LAG Sbjct: 194 AMVHAIESYTSASANNNPVSKALAREALRLLGANIETAVKDGSNVKARSDMLLGAMLAGQ 253 Query: 254 AFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMA----DIFNALG 309 AF N+ VA VHALAYP+GG FH+ HG SNA++LP+VM + + C + + D+F L Sbjct: 254 AFANSPVAAVHALAYPIGGIFHVPHGLSNALVLPHVMRFNTEICGEAYSILATDVFPDLA 313 Query: 310 GNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSP 369 G + + + + ++ LE AD+G+ +TL GI E+ L +L D+++Q RLL +P Sbjct: 314 GTPA----AKRANQFIDRLEALSADLGLEQTLREVGIGEADLATLASDSMKQTRLLVNNP 369 Query: 370 LPLLEADIRAIYEAAF 385 + E D AIY+AAF Sbjct: 370 REVSETDALAIYKAAF 385 Lambda K H 0.318 0.135 0.381 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 363 Number of extensions: 21 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 395 Length of database: 385 Length adjustment: 31 Effective length of query: 364 Effective length of database: 354 Effective search space: 128856 Effective search space used: 128856 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory